The Premier League has confirmed it will not sit on the Football Association's commission into the declining number of England-qualified players selected in Premier League teams.

On Wednesday, the FA chairman, Greg Dyke, will provide more detail on his commission, which he announced last month, but the Premier League chairman will not formally be part of it. The Premier League has said its level of involvement will depend on the detail about the scope of the commission which Dyke has yet to present.

Dyke is establishing the commission to address what he described as "an issue almost everyone involved in football knows is the biggest problem the England team faces". Dyke then made it clear he had "invited the chairmen of both the Premier League and the Football League to join the commission, along with the chairmen of the League Managers Association and the Professional Footballers Association".

After the Premier League meeting a week later, which Dyke attended and at which he was heard, according to senior club figures present, mostly in stony silence, a statement was issued which said: "The Premier League clubs today met and affirmed their commitment to engaging in a collaborative and co-operative manner with the debate and process outlined by the FA chairman in his recent speech."

There was a quote from Dyke saying: "I am pleased that the Premier League clubs, board and executive all want to contribute to the commission I am setting up."

The truth, however, is that the recently appointed Premier League chairman, the investment banker Anthony Fry, had declined the FA chairman's invitation to sit on the commission. The Premier League has also declined to explain why it has chosen to remain on the outside, a stance recommended by the league's chief executive, Richard Scudamore, club sources said.

The Football League chairman, Greg Clarke, has enthusiastically accepted, and Dyke is expected to confirm that the LMA and PFA chairmen have accepted their invitations.

The commission, intended to be an honest examination into why just 32% of players in Premier League starting teams last season were England-qualified, and the overwhelming majority of players bought this summer were from overseas, will not primarily focus on youth development, Dyke suggested. A revamped youth system, the elite player performance plan (EPPP), was introduced at the Premier League's insistence throughout football the year before last, and there will be no overhaul until enough time has elapsed for it to be judged.

Dyke, who spent weeks at the start of his tenure talking to people about English football's challenges, focused instead on several factors which have long felt unsayable, given the Premier League's financial and administrative power. Some people, he said, "say the problem of having so many foreign players is caused by the owners of Premier League clubs who are so impatient for success that no manager dare take a chance on English kids". Others, he said, "argue that if your top league is largely foreign-owned with foreign managers why should those in control care about developing the England team?"

There are divergent views even within the Premier League about why Scudamore then recommended Fry should not accept Dyke's invitation to sit on such an inquiry. Insiders say the atmosphere for Dyke at the subsequent Premier League meeting was frosty, and that his contribution was subdued. Margaret Byrne, the Sunderland chief executive, reacted angrily to Dyke having pointed in his public speech to her club signing 14 players this summer for the then manager, Paolo Di Canio, of whom only one was English.

Byrne wrote in the club's programme for Sunderland's next home match against Arsenal: "I was very disappointed by some comments in Mr Dyke's speech and in particular his reference to Sunderland."

Byrne wrote that several of the 14 signed would form a "shadow" development squad, and she stressed that the investment in the EPPP demonstrated that clubs do want to develop English players: "I am sure that when Mr Dyke has had an opportunity to speak with clubs and to familiarise himself with the rigorous process involved with EPPP, he will become more knowledgeable as to the efforts that we are making."

That rebuke, the implication that Dyke should have spoken to the clubs first – and arguing that youth development is the only issue, not foreign owners building global brands – has so far spoken for the other Premier League clubs. Some privately question the FA's contribution to coaching, facilities and development, and grumble that Dyke should be addressing that before pointing the finger at their selection of players.

The other public responses came from managers, Arsène Wenger and Roberto Martínez, who stunned the Football League by suddenly talking about wanting lower division clubs as "feeder" clubs for the Premier League. That idea, for an even further extension of power, has a surprising degree of support among the Premier League clubs. Those who acknowledge there is a problem giving young players aged 18-22 experience at clubs which can afford to buy the world's mature best stars, say they would like to use a Barnet, or an Accrington Stanley, for that purpose.

That prompted an adamant defence by Clarke, who is celebrating the Football League's 125th year since its foundation in 1888.

"The commission must consider all ideas, but Football League clubs are not interested in being relegated to subsidiaries of Premier League clubs," he said. "That would undermine 125 years of tradition and clubs being at the heart of their communities. We should appreciate the depth English professional football has, which no other country can match."

The net result of Greg Dyke's first practical primer in football's realities is that the FA chairman's inquiry into why the Premier League selects so few of the England-qualified young players who its clubs train for years, will take place without the Premier League on his commission.

In his first public speech, Dyke promised to confront the difficult questions, and one of the answers, immediately, was that he needs to know the FA's place.